title: Genetic algorithm solution for partial digest problem.
abstract: One of the fundamental problems in computational biology is the construction of physical maps of chromosomes from the hybridisation experiments between unique probes and clones of chromosome fragments. Before introducing the shotgun sequencing method, Partial Digest Problem (PDP) was an intractable problem used to construct the physical maps of DNA sequence in molecular biology. In this paper, we develop a novel Genetic Algorithm (GA) for solving the PDP. This algorithm is implemented and compared with well-known existing algorithms on different types of random and real instances data, and the obtained results show the efficiency of our algorithm. Also, our GA is adapted to handle the erroneous data and their efficiency is presented for the large instances of this problem.
authors.affiliation: School of Mathematics, Statistics and Computer Science, University of Tehran, Tehran, Iran.
authors.forename: Hayedeh
authors.initials: H
authors.lastname: Ahrabian
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ganjtabesh
authors.forename: Abbas
authors.initials: A
authors.lastname: Nowzari-Dalini
authors.forename: Zahra
authors.initials: Z
authors.lastname: Razaghi-Moghadam-Kashani
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D023281:Genomics / Q000379:methods*
keywords: DNA sequencing; GAs; PDP; bioinformatics; genetic algorithms; partial digest problem